rs1009592

Variant names:

• chr1-11868657-C-G
• rs1009592

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.415 in 152,050 control chromosomes in the GnomAD database, including 14,375 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.41 (14375 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63019 AN: 151932 Hom.: 14337 Cov.: 31

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.400

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.415 AC: 63100 AN: 152050 Hom.: 14375 Cov.: 31 AF XY: 0.408 AC XY: 30290 AN XY: 74326

African (AFR) AF: 0.607 AC: 25175 AN: 41458

American (AMR) AF: 0.277 AC: 4235 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3472

East Asian (EAS) AF: 0.200 AC: 1032 AN: 5166

South Asian (SAS) AF: 0.443 AC: 2137 AN: 4824

European-Finnish (FIN) AF: 0.293 AC: 3093 AN: 10564

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.366 AC: 24892 AN: 67978

Other (OTH) AF: 0.399 AC: 842 AN: 2108

Alfa AF: 0.381 Hom.: 1566

Bravo AF: 0.419

Asia WGS AF: 0.372 AC: 1292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.17
PhyloP100		-0.97

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1009592; hg19: chr1-11928714; COSMIC: COSV59923975;